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With the program RasMol, you can select, as Mad Scientist explained it for PyMol, everything in a specific distance around an atom. RasMol can be run from command line, using a script (with the -script option under UNIX).

These two links go through the specifications required for the PDB format:
Link1: http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
Link1 primarily goes through the specs. required if you say have a NMR file you would therefore require the MODEL statement. It also goes through other statements such as when to use TER and how each ATOM line should look ...

Not quite as ideal as I had hoped, but it works:
Get and install CCP4.
Obtain minimal CIF file from PDB or elsewhere. Save to some folder easy to get at with the console.
Launch console and cd to folder with the minimal definition.
Run libcheck by typing it and hitting return
If it complains it's not found, the CCP4 bin directory may not be in your ...